4XQB

CRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH TRIVALENT SIALIC ACID INHIBITOR ME0461


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.597 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Triazole linker-based trivalent sialic acid inhibitors of adenovirus type 37 infection of human corneal epithelial cells.

Caraballo, R.Saleeb, M.Bauer, J.Liaci, A.M.Chandra, N.Storm, R.J.Frangsmyr, L.Qian, W.Stehle, T.Arnberg, N.Elofsson, M.

(2015) Org.Biomol.Chem. 13: 9194-9205

  • DOI: 10.1039/c5ob01025j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Adenovirus type 37 (Ad37) is one of the principal agents responsible for epidemic keratoconjunctivitis (EKC), a severe ocular infection that remains without any available treatment. Recently, a trivalent sialic acid derivative (ME0322, Angew. Chem. I ...

    Adenovirus type 37 (Ad37) is one of the principal agents responsible for epidemic keratoconjunctivitis (EKC), a severe ocular infection that remains without any available treatment. Recently, a trivalent sialic acid derivative (ME0322, Angew. Chem. Int. Ed., 2011, 50, 6519) was shown to function as a highly potent inhibitor of Ad37, efficiently preventing the attachment of the virion to the host cells and subsequent infection. Here, new trivalent sialic acid derivatives were designed, synthesized and their inhibitory properties against Ad37 infection of the human corneal epithelial cells were investigated. In comparison to ME0322, the best compound (17a) was found to be over three orders of magnitude more potent in a cell-attachment assay (IC50 = 1.4 nM) and about 140 times more potent in a cell-infection assay (IC50 = 2.9 nM). X-ray crystallographic analysis demonstrated a trivalent binding mode of all compounds to the Ad37 fiber knob. For the most potent compound ophthalmic toxicity in rabbits was investigated and it was concluded that repeated eye administration did not cause any adverse effects.


    Organizational Affiliation

    Department of Chemistry, Umeå University, SE90187 Umeå, Sweden. mikael.elofsson@chem.umu.se.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fiber
A, B, C
194Human adenovirus D37Mutation(s): 0 
Gene Names: L5
Find proteins for Q64823 (Human adenovirus D37)
Go to UniProtKB:  Q64823
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
425
Query on 425

Download SDF File 
Download CCD File 
A
2-(1-{2-[bis(2-{4-[2-({(6R)-5-(acetylamino)-3,5-dideoxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-beta-L-threo-hex-2-ulopyranonosyl}oxy)ethyl]-1H-1,2,3-triazol-1-yl}ethyl)amino]ethyl}-1H-1,2,3-triazol-4-yl)ethyl (6R)-5-(acetylamino)-3,5-dideoxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-beta-L-threo-hex-2-ulopyranosidonic acid
C51 H81 N13 O27
BLJKNJLUKOGWGY-UYSYNVRDSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.597 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.440α = 90.00
b = 70.320β = 94.47
c = 74.480γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB 685
Swedish Research CouncilSweden521-2010-3078
Swedish Research CouncilSweden621-2010-4746
Knut and Alice Wallenberg FoundationSweden2009.0009
Stiftelsen foer Strategisk ForskningSwedenF06-0011
Torsten Soederbergs StiftelseSwedenM4/11

Revision History 

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-09-02
    Type: Database references
  • Version 2.0: 2017-09-06
    Type: Advisory, Atomic model, Author supporting evidence, Derived calculations